DNA Sequencing of Deadly Bacteria May Help Prevent Outbreaks

The Gist

Several retrospective studies have successfully tracked the spread of diseases between patients at healthcare facilities by sequencing the genomes of infectious bacteria, according to a new "Perspective" in Science by researchers at the University of Queensland. In these studies, epidemic strains such as E. coli and Streptococcus were investigated during outbreaks in hospitals and clinics. Researchers were able to reconstruct the pathways of transmission by identifying variations and similarities in the bacteria’s genetic code.

“These types of studies are being used to characterize outbreaks of infectious microorganisms, and trace their spread,” said report co-author Mark Walker, Director of the Australian Infectious Disease Research Centre at the University of Queensland.

Every year in the United States, 100,000 deaths are attributed to infectious diseases contracted in facilities like hospitals, clinics, medical centers, and nursing homes despite standard measures taken to prevent such occurrences. Some of the bacteria causing these diseases are so called “super bugs,” such as the highly antibiotic-resistant Staphylococcus aureus. By better understanding the spread of microbes, and being able to monitor that spread at the genetic level, healthcare providers may be able to prevent some of those deaths, according to the report’s authors.

The Expert Take

“Application of whole genome sequencing, in the clinical epidemiology context, will help hospital and healthcare facilities track the spread of hospital-acquired infections, leading to better management practices,” said Walker.

Knowledge gleaned from gene sequencing has been used to develop new methods of diagnosis and approaches to fighting infections.

“This information will allow us to detect carriers in the hospital environment, leading to treatment and eradication of the reservoir of infection,” said Walker.

Source and Method

DNA sequencing technologies were used in several studies to track harmful and antibiotic-resistant bacteria in healthcare facilities. Study subjects included, among others, the spread of Klebsiella pneumoniae at the National Institutes of Health Clinical Center, which claimed 11 patients; an outbreak of Staphylococcus aureus (MRSA, or golden staph) among infants in a hospital in Cambridge, UK; and a rash of Streptococcus pyogenes (often responsible for “strep throat,” but in this case for deadly infections after child birth) in Australian hospitals.

These kinds of bacteria are responsible for hundreds of thousands of deaths each year.

The Takeaway

The report’s authors advocate more widespread use of gene sequencing of pathogens as a tool for prevention. Research suggests that in the future, with the development of software and protocols, real-time gene sequencing of pathogenic bacteria could lead to knowledge of identifiable antibiotic resistances, early detection of virulent strains, and same-day diagnosis of infections. Vaccines are already being developed based on gene sequencing for use against various diseases such as meningitis, which leads to fatality amongst children.

“However,” the report’s authors point out, “hospitals must be funded, staffed, and equipped to do this kind of investigation and analysis in real time. Most hospitals are simply not equipped to generate and analyze such data.”

As technology costs decrease and sequencing data and analysis become widespread, more healthcare facilities may adopt these methods. Eventually this may lead to lower rates of infection and fewer deaths.

Other Research

A 2010 study in Science documented the rapid evolution of Streptococcus pneumoniae in response to application of vaccines.

In 2012, a PLOS Pathogensstudy reported on the dramatic drop in cost, and thus accessibility, of gene sequencing technologies.

A 2011 report in Nature examined the diversity of the microbial population of healthy humans.

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